Main
Kasia Kedzierska
I am a 3rd year PhD student at the University of Oxford. I am a computational biologist, i.e., I use Data Science and Statistical Machine Learning to answer biological questions. Specifically, I study cancer of the uterus and chromatin organisation in disease progression. To efficiently preprocess terabytes of data, I take advantage of Bash/Awk oneliners and scripts. Then, I analyse and visualise preprocessed data in R and Python.
I like teaching and deeply believe in Open Science. With #NGSchool Society which I’m the president of I’ve been organising Summer Schools in Bioinformatics. During last year edition - #NGSchool2019: Machine Learning for Biomedicine we recorded and published some of the lectures. This year, because of the pandemic, we switched to organising virtual events - NGSeminars series. We made all the content publicly available.
Selected Research Experience
DPhil Candidate
Church group @ Wellcome Centre for Human Genetics, Wedge group @ Big Data Institute
University of Oxford, UK
2022 - 2018
- PhD project: Functional and evolutionary characterisation of chromatin organisation in endometrial cancer
Education
DPhil. Candidate, Genomic Medicine and Statistics
Nuffield Department of Medicine, Brasenose College
University of Oxford, UK
2022 - 2018
- PhD fully funded by Wellcome Trust Four-year PhD Studentships in Science
M. Sc. Eng., Biotechnology
Warsaw University of Technology
Warsaw, Poland
2018 - 2015
- Thesis: Analysis of the mutational burden across gene sets in cancer.
- Thesis awarded the best Master thesis in Bioinformatics defended in 2018 title.
Selected Publications
The MLH1 polymorphism rs1800734 and risk of endometrial cancer with microsatellite instability
H. Russell, K. Kedzierska, D. D. Buchanan, R. Thomas, E. Tham, M. Mints, A. Keränen, G. G. Giles, M. C. Southey, R. L. Milne, I. Tomlinson, D. Church, A. B. Spurdle, T. A. O’Mara and A. Lewis
Clinical Epigenetics
2020
Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development
M. Pawlak, K. Z. Kedzierska, M. Migdal, K. A. Nahia, J. A. Ramilowski, L. Bugajski, K. Hashimoto, A. Marconi, K. Piwocka, P. Carninci and C. L. Winata
Genome Research
2019
Genomic analysis of DNA repair genes and androgen signaling in prostate cancer
K. Jividen, K. Z. Kedzierska, C.-S. Yang, K. Szlachta, A. Ratan and B. M. Paschal
BMC Cancer
2018
SONiCS: PCR stutter noise correction in genome-scale microsatellites
K. Z. Kedzierska, L. Gerber, D. Cagnazzi, M. Krützen, A. Ratan, L. Kistler
Bioinformatics
2018
Selected Talks and Posters
Analysis of the mutational burden across gene sets in cancer
Polish Bioinformatics Society Symposium
Cracow, Poland
2019
- Invited talk
Differential mutation analysis across gene sets in cancers
The Biology of Genomes 2018
Cold Spring Harbor, NY, USA
2018
- Poster
Selected Awards and Honours
Best Master Thesis in Bioinformatics
N/A
N/A
2019 - 2018
- The Best Master Thesis defended in the field of Bioinformatics in 2018 in Poland.
- Analysis of the mutational burden across gene sets in cancer Master thesis defended at the Warsaw University of Technology
Teaching Experience
Online tutorials: Python for Data Science and Introduction to Python
YouTube
2020
- I led two Python tutorials: Introduction to Python kasia.codes/talk/intro_to_python/ and Python for Data Science kasia.codes/talk/py4ds/.
Introduction to Managing Code with Git
Wellcome Centre for Human Genetics
Oxford, United Kingdom
2020 - 2019
- I led a 2-hour introduction to working with Git. Materials, including slides and exercises are available at kasia.codes/talk/into_to_git/.
Unsupervised learning, Introduction to Python
#NGSchool2019: Machine Learning for Biomedicine
Ostróda, Poland
2019
- Tutor for the Introduction to Python (3 h workshop) and for the Unsupervised learning (1,5 h lecture).
- Materials for the Introduction to Python are available on github
Introduction to R
Wellcome Centre for Human Genetics
Oxford, United Kingdom
2019
- 8 week course in Introduction to R, Data Manipulation, Data Visualisation and RNA-seq data analysis.
- Materials available on github/kzkedziersa/r_intro
Attended Workshops, Summer Schools
Machine Learning Summer School
Imperial College London, University College Londn
London, United Kingdom
2019
Selected Grants
Visegrad Grant to organize #NGSchool2020 - postponed until 2021
N/A
2021 - 2020
- 32,190 EUR awarded towards organising #NGSchool2020 and #NGSymposium. Both events are postponed until 2021.
Non-profit Work
President
N/A
2021 - 2018
- The goal of the Society is to promote and support science, with emphasis on computational biology.
- President since 2019; Vice President 2018 - 2019